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Ruth

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Ruth
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  • Thanks for getting back to me @Sheila. Just to clarify, I am not looking to mask indels, only low confidence positions throughout the genome, regardless of whether they are SNVs. These are likely the same as the reference, however due to low confide…
  • Hi, I just downloaded the nightly build and re-ran FastaAlternateReferenceMaker and the same problem still occurs. Thanks, Ruth
  • Hi, I believe I have a similar problem, which does not seem to be resolved. I have run VariantAnnotator with --allSites, then VariantFiltration to indicate any positions (SNV or not) that does not pass my filtration thresholds. I then made a s…
  • That is exactly what I need. Thank you very much for your help. Ruth
  • Hi, My aim is to generate a complete genome sequence for each of my samples. I don't want to assume the reference sequence for all positions that are not SNVs, so I wanted to generate a gVCF file, so that I can then run the VariantAnnotator on ev…
  • Hi, Yes, it seems to work OK if I run GenotypeGVCFs first. I just put one --variant in (which was my vcf file). However, running this looses a lot of information, as my vcf file now has a lot fewer lines (57985 as opposed to 554164) Is there…
  • Hi, Thanks for getting back to me. You are right, the vcf file does fail validation - with the error: ERROR MESSAGE: File /projects4/ruth/Burkholderia/cutadapt/cenocepacia/bowtie/N501.C8967_R1.fastq_to_B_cenocepacia_J2315.sorted_GATK.vcf fail…